JAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignm...

[jalview.git] / test / jalview / io / CrossRef2xmlTests.java

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 67626c8..080bda8 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -52,6 +52,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Operational" }, enabled = true)
   public void testRetrieveAndShowCrossref() throws Exception
   {
+
+    List<String> failedDBRetr = new ArrayList<String>();
     List<String> failedXrefMenuItems = new ArrayList<String>();
     List<String> failedProjectRecoveries = new ArrayList<String>();
 
@@ -75,7 +77,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     List<String> keyseq = new ArrayList<String>();
     HashMap<String, File> savedProjects = new HashMap<String, File>();
 
-    for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+    for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+    { "UNIPROT", "P01731" } })
     {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
@@ -97,16 +100,23 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
         {
           // retrieve dbref
 
+          List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+                  did[0], did[1]);
+          if (afs.size() == 0)
+          {
+            failedDBRetr.add("Didn't retrieve " + first);
+            break;
+          }
           keyseq.add(first);
-
-          af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
-                  .get(0);
-          Assert.assertTrue(af != null, "Didn't retrieve " + first);
+          af = afs.get(0);
 
           // verify references for retrieved data
           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
                   + pass3 + "): Fetch " + first + ":");
+          AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Fetch " + first + ":");
           dna = af.getViewport().getAlignment().isNucleotide();
           retral = af.getViewport().getAlignment();
           dataset = retral.getDataset();
@@ -130,6 +140,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
                   + pass3 + "): Recover " + first + ":");
+          AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Recover " + first + ":");
 
         }
 
@@ -222,6 +235,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                       "Pass (" + pass1 + "," + pass2 + "," + pass3
                               + "): before start of pass3: " + nextxref
                               + ":");
+              AlignmentTest.assertDatasetIsNormalised(avp.getAlignment(),
+                      "Pass (" + pass1 + "," + pass2 + "," + pass3
+                              + "): before start of pass3: " + nextxref
+                              + ":");
 
               SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
 
@@ -334,6 +351,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                             nextavp.getAlignment(), "" + "Pass (" + pass1
                                     + "," + pass2 + "): For "
                                     + nextnextxref + ":");
+                    AlignmentTest.assertDatasetIsNormalised(
+                            nextavp.getAlignment(), "" + "Pass (" + pass1
+                                    + "," + pass2 + "): For "
+                                    + nextnextxref + ":");
 
                     stringify(dbtoviewBit, savedProjects, nextnextxref,
                             nextavp);
@@ -369,10 +390,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
         }
         else
         {
-          // verify stored projects for second set of cross references
-          pass2 = 1;
+          pass1++;
+          if (pass1 < 2)
+          {
+            // verify stored projects for second set of cross references
+            pass2 = 1;
           // and verify cross-references retrievable from those stored projects.
-          pass3 = 0;
+            pass3 = 0;
+          }
         }
       } while (pass3 < 2);
     }
@@ -395,6 +420,15 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
               + failedProjectRecoveries.size() + " counts)");
     }
+    if (failedDBRetr.size() > 0)
+    {
+      for (String s : failedProjectRecoveries)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+              + failedDBRetr.size() + " counts)");
+    }
   }
 
   private void assertProtein(AlignmentViewPanel alignmentViewPanel,